Made some documentation updates & fixes
--Mostly doc block tweaks --Added @DocumentedGATKFeature to some walkers that were undocumented because they were ending up in "uncategorized". Very important for GSA: if a walker is in public or protected, it HAS to be properly tagged-in. If it's not ready for the public, it should be in private.
This commit is contained in:
Geraldine Van der Auwera
parent
c813259283
commit
95a9ed853d
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@ -70,10 +70,11 @@ import java.util.Map;
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/**
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* Total (unfiltered) depth over all samples.
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*
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* While the sample-level (FORMAT) DP field describes the total depth of reads that passed the Unified Genotyper's
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* <p>While the sample-level (FORMAT) DP field describes the total depth of reads that passed the caller's
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* internal quality control metrics (like MAPQ > 17, for example), the INFO field DP represents the unfiltered depth
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* over all samples. Note though that the DP is affected by downsampling (-dcov), so the max value one can obtain for
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* N samples with -dcov D is N * D
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* </p>
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*/
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public class Coverage extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
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@ -69,10 +69,15 @@ import java.util.*;
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/**
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* Phred-scaled p-value using Fisher's Exact Test to detect strand bias (the variation
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* being seen on only the forward or only the reverse strand) in the reads? More bias is
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* indicative of false positive calls. Note that the fisher strand test may not be
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* calculated for certain complex indel cases or for multi-allelic sites.
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* Phred-scaled p-value using Fisher's Exact Test to detect strand bias
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*
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* <p>Phred-scaled p-value using Fisher's Exact Test to detect strand bias (the variation
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* being seen on only the forward or only the reverse strand) in the reads. More bias is
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* indicative of false positive calls.
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* </p>
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*
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* <h3>Caveat</h3>
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* <p>The Fisher Strand test may not be calculated for certain complex indel cases or for multi-allelic sites.</p>
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*/
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public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
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private final static Logger logger = Logger.getLogger(FisherStrand.class);
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@ -68,7 +68,7 @@ import java.util.Map;
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/**
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* GC content of the reference around this site
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* GC content of the reference around the given site
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*
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* <p>The GC content is the number of GC bases relative to the total number of bases (# GC bases / # all bases) around this site on the reference.</p>
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*
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@ -61,7 +61,7 @@ import java.util.List;
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* User: rpoplin
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* Date: Nov 27, 2009
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*
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* A collection of the arguments that are common to both CovariateCounterWalker and TableRecalibrationWalker.
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* A collection of the arguments that are used for BQSR. Used to be common to both CovariateCounterWalker and TableRecalibrationWalker.
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* This set of arguments will also be passed to the constructor of every Covariate when it is instantiated.
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*/
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@ -131,14 +131,14 @@ public class RecalibrationArgumentCollection {
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public boolean RUN_WITHOUT_DBSNP = false;
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/**
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* CountCovariates and TableRecalibration accept a --solid_recal_mode <MODE> flag which governs how the recalibrator handles the
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* BaseRecalibrator accepts a --solid_recal_mode <MODE> flag which governs how the recalibrator handles the
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* reads which have had the reference inserted because of color space inconsistencies.
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*/
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@Argument(fullName = "solid_recal_mode", shortName = "sMode", required = false, doc = "How should we recalibrate solid bases in which the reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS")
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public RecalUtils.SOLID_RECAL_MODE SOLID_RECAL_MODE = RecalUtils.SOLID_RECAL_MODE.SET_Q_ZERO;
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/**
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* CountCovariates and TableRecalibration accept a --solid_nocall_strategy <MODE> flag which governs how the recalibrator handles
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* BaseRecalibrator accepts a --solid_nocall_strategy <MODE> flag which governs how the recalibrator handles
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* no calls in the color space tag. Unfortunately because of the reference inserted bases mentioned above, reads with no calls in
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* their color space tag can not be recalibrated.
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*/
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@ -47,6 +47,7 @@
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package org.broadinstitute.sting.gatk.walkers.bqsr;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.CommandLineGATK;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.filters.*;
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@ -55,18 +56,27 @@ import org.broadinstitute.sting.gatk.report.GATKReport;
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import org.broadinstitute.sting.gatk.report.GATKReportTable;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
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import org.broadinstitute.sting.utils.help.HelpConstants;
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import org.broadinstitute.sting.utils.recalibration.*;
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import java.io.*;
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/**
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* Evaluate the performance of the base recalibration process
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*
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* <p>This tool aims to evaluate the results of the Base Quality Score Recalibration (BQSR) process.</p>
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*
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* <h3>Caveat</h3>
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* <p>This tool is currently experimental. We do not provide documentation nor support for its operation.</p>
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*
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*/
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@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
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@ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class, UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class})
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@PartitionBy(PartitionType.READ)
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public class RecalibrationPerformance extends RodWalker<Integer, Integer> implements NanoSchedulable {
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@Output(doc="Write output to this file")
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@Output
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public PrintStream out;
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@Input(fullName="recal", shortName="recal", required=false, doc="The input covariates table file")
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@ -48,6 +48,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.CommandLineGATK;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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@ -55,6 +56,8 @@ import org.broadinstitute.sting.gatk.report.GATKReport;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
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import org.broadinstitute.sting.utils.help.HelpConstants;
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import java.io.PrintStream;
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import java.util.ArrayList;
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@ -63,11 +66,11 @@ import java.util.LinkedList;
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import java.util.Map;
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/**
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* Simple walker to plot the coverage distribution per base.
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* Simple walker to plot the coverage distribution per base
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*
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* <p>
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* Features of this walker:
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* <li>includes a smart counting of uncovered bases without visiting the uncovered loci.</li>
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* <li>includes a smart counting of uncovered bases without visiting the uncovered loci</li>
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* <li>includes reads with deletions in the loci (optionally can be turned off)</li>
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* </p>
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*
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@ -91,10 +94,11 @@ import java.util.Map;
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* -fd \
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* -o report.grp
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* </pre>
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* User: carneiro
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* Date: 1/27/13
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* Time: 11:16 AM
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*
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* @author carneiro
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* @since 1/27/13
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*/
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@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
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public class BaseCoverageDistribution extends LocusWalker<ArrayList<Integer>, Map<Integer, ArrayList<Long>>> {
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/**
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* The output GATK Report table
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@ -82,7 +82,7 @@ import java.util.*;
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*
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* This helper class holds the data HashMap as well as submaps that represent the marginal distributions collapsed over all needed dimensions.
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* It also has static methods that are used to perform the various solid recalibration modes that attempt to correct the reference bias.
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* This class holds the parsing methods that are shared between CountCovariates and TableRecalibration.
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* This class holds the parsing methods that are shared between BaseRecalibrator and PrintReads.
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*/
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public class RecalUtils {
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@ -117,7 +117,7 @@ import java.util.*;
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// todo -- alter logarithmic scaling to spread out bins more
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// todo -- allow for user to set linear binning (default is logarithmic)
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// todo -- formatting --> do something special for end bins in getQuantile(int[] foo), this gets mushed into the end+-1 bins for now
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@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} )
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@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
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@By(DataSource.REFERENCE)
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@PartitionBy(PartitionType.NONE)
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@Downsample(by= DownsampleType.NONE, toCoverage=Integer.MAX_VALUE)
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@ -29,12 +29,15 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.ArgumentCollection;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.CommandLineGATK;
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import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
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import org.broadinstitute.sting.utils.help.HelpConstants;
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import org.broadinstitute.variant.variantcontext.Genotype;
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import org.broadinstitute.variant.variantcontext.GenotypesContext;
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import org.broadinstitute.variant.variantcontext.VariantContext;
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@ -44,12 +47,15 @@ import java.io.*;
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import java.util.Collection;
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/**
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* print intervals file with all the variant sites that have "most" ( >= 90% by default) of the samples with "good" (>= 10 by default)coverage ("most" and "good" can be set in the command line).
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* Print intervals file with all the variant sites for which most of the samples have good coverage
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*
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* <p>
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* CoveredByNSamplesSites is a GATK tool for filter out sites based on their coverage.
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* CoveredByNSamplesSites is a GATK tool for filtering out sites based on their coverage.
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* The sites that pass the filter are printed out to an intervals file.
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*
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* See argument defaults for what constitutes "most" samples and "good" coverage. These parameters can be modified from the command line.
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* </p>
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*
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* <h3>Input</h3>
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* <p>
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* A variant file and optionally min coverage and sample percentage values.
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@ -60,7 +66,7 @@ import java.util.Collection;
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* An intervals file.
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* </p>
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*
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* <h3>Examples</h3>
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* <h3>Example</h3>
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* <pre>
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* java -Xmx2g -jar GenomeAnalysisTK.jar \
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* -R ref.fasta \
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@ -71,7 +77,7 @@ import java.util.Collection;
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* </pre>
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*
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*/
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@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
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@By(DataSource.REFERENCE_ORDERED_DATA)
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public class CoveredByNSamplesSites extends RodWalker<GenomeLoc, Integer> implements TreeReducible<Integer> {
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@ -26,6 +26,7 @@
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package org.broadinstitute.sting.gatk.walkers.variantutils;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.CommandLineGATK;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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@ -33,6 +34,8 @@ import org.broadinstitute.sting.gatk.report.GATKReport;
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import org.broadinstitute.sting.gatk.report.GATKReportTable;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
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import org.broadinstitute.sting.utils.help.HelpConstants;
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import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
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import org.broadinstitute.variant.variantcontext.*;
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import org.broadinstitute.variant.vcf.VCFHeader;
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@ -41,29 +44,30 @@ import java.io.PrintStream;
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import java.util.*;
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/**
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* A simple walker for performing genotype concordance calculations between two callsets. Outputs a GATK table with
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* per-sample and aggregate counts and frequencies, a summary table for NRD/NRS, and a table for site allele overlaps.
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* Genotype concordance (per-sample and aggregate counts and frequencies, NRD/NRS and site allele overlaps) between two callsets
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*
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* <p>
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* Genotype concordance takes in two callsets (vcfs) and tabulates the number of sites which overlap and share alleles,
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* GenotypeConcordance takes in two callsets (vcfs) and tabulates the number of sites which overlap and share alleles,
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* and for each sample, the genotype-by-genotype counts (for instance, the number of sites at which a sample was
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* called homozygous reference in the EVAL callset, but homozygous variant in the COMP callset). It outputs these
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* counts as well as convenient proportions (such as the proportion of het calls in the EVAL which were called REF in
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* the COMP) and metrics (such as NRD and NRS).
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*
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* <h2> INPUT </h2>
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* <h3>Input</h3>
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* <p>
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* Genotype concordance requires two callsets (as it does a comparison): an EVAL and a COMP callset, specified via
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* the -eval and -comp arguments
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* <p>
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* the -eval and -comp arguments.
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*
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* (Optional) Jexl expressions for genotype-level filtering of EVAL or COMP genotypes, specified via the -gfe and
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* -cfe arguments, respectively.
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* </p>
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*
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* <h2> OUTPUT </h2>
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* Genotype Concordance writes a GATK report to the specified (via -o) file, consisting of multiple tables of counts
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* <h3>Output</h3>
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* Genotype Concordance writes a GATK report to the specified file (via -o) , consisting of multiple tables of counts
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* and proportions. These tables may be optionally moltenized via the -moltenize argument.
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*
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*/
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@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
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public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,VariantContext>>,ConcordanceMetrics> {
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/**
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